Robust diagnosis and meta visualizations of plant diseases through deep neural architecture with explainable AI

Deep learning has emerged as a highly effective and precise method for classifying images. The presence of plant diseases poses a significant threat to food security. However, accurately identifying these diseases in plants is challenging due to limited infrastructure and techniques. Fortunately, the recent advancements in deep learning within the field of computer vision have opened up new possibilities for diagnosing plant pathology. Detecting plant diseases at an early stage is crucial, and this research paper proposes a deep convolutional neural network model that can rapidly and accurately identify plant diseases. Given the minimal variation in image texture and color, deep learning techniques are essential for robust recognition. In this study, we introduce a deep, explainable neural architecture specifically designed for recognizing plant diseases. Fine-tuned deep convolutional neural network is designed by freezing the layers and adjusting the weights of learnable layers. By extracting deep features from a down sampled feature map of a fine-tuned neural network, we are able to classify these features using a customized K-Nearest Neighbors Algorithm. To train and validate our model, we utilize the largest standard plant village dataset, which consists of 38 classes. To evaluate the performance of our proposed system, we estimate specificity, sensitivity, accuracy, and AUC. The results demonstrate that our system achieves an impressive maximum validation accuracy of 99.95% and an AUC of 1, making it the most ideal and highest-performing approach compared to current state-of-the-art deep learning methods for automatically identifying plant diseases.

Modern agricultural techniques and tools have revolutionized food production, allowing us to meet the evergrowing demands of the world's population.However, this progress is threatened by two major factors: climate change and plant disease.Climate change, as highlighted by Tai 1 , poses a significant risk to food production.Additionally, plant diseases, as noted by Strange 2 , also jeopardize our ability to meet global food requirements.The impact of plant diseases extends beyond the global scale; it has severe consequences for smallholder farmers who make up more than 80% of agricultural production 3 .Shockingly, half of the world's hungry people reside in smallholder farmer households 4 .The presence of plant diseases can have a devastating effect on agricultural production, and if left undetected over time, it will exacerbate food insecurity 5 .To ensure a consistent food supply, it is crucial to detect and prevent plant diseases at an early stage.This task, however, presents challenges in rural regions of developing countries where farmers have limited access to agricultural experts.Therefore, there is a pressing need for automatic and efficient methods of detecting plant diseases in their early stages.
Different approaches, ranging from historical to modern, are utilized to prevent crop loss caused by plant diseases.Regardless of the specific methods employed 6 , the accurate and early identification of plant diseases is crucial for effective mitigation.The advancement of image classification has opened up new possibilities for applying computer vision research in the field of agriculture [7][8][9] .Deep learning models can now be employed to detect and classify plant diseases using images.This paper presents the development of a graph-based deep learning model that enables accurate and rapid diagnosis of plant diseases.Researchers have made significant advancements in the field of plant or leaf recognition by employing a range of autonomous systems.These systems often utilize deep learning and machine learning techniques to tackle this challenge effectively.To establish a robust classification system for plant diseases, it is imperative to train it on a comprehensive dataset that encompasses noisy images.Given the scarcity of manual professionals in densely populated countries like India, the development of an Artificial Intelligence-driven tool for identifying plants holds immense significance.The main contributions of this study can be summarized as follows: • Deep Fused convolutional Neural Network and customized K-nearest Neighbor-based framework is pro- posed for the precise classification of plant diseases based on leaf images.This framework employs depthwise separable convolution to generate optimal feature maps on leaf images, enhancing multi-class classification.• A dataset preparation pipeline is established for plant village dataset, facilitating the extraction of patches from high-density pixel images.• Design of Meta agnostic model learning by Grad-CAM and Occulusion Sensitivity Analysis(OSA) to identify the parts of an image that influenced the model's labeling decision • The proposed framework thoroughly investigates the impact of fused features and customized KNN on classification performance, demonstrating that the model achieves the highest metrics in terms of accuracy, sensitivity, and specificity.The comprehensive investigation and comparative analysis underscore the efficacy of the proposed framework over other state-of-the-art methods.
The organization of this document is as follows.In Section "Related Work", the most recent algorithms for machine learning and deep learning in the classification of plant diseases are presented.Section "Proposed HerbNet framework" introduces the HerbNet model, which is specifically designed for classifying the leaves of plant diseases.This section also provides a comprehensive description of the plant diseases used in this research.The experimental work and performance evaluation of the proposed system are elaborated in Section "Results and discussion".Lastly, Section."Conclusion" concludes the paper and discusses future directions.

Related work
Plenty of researchers are currently exploring research-based image classification using medical images and satellite images.However, the classification of plant images based on leaves is still limited.In this study, my focus is on plant image classification using machine learning and deep learning techniques.

Machine learning (ML) based techniques for plants disease identification
Aurangzeb et al. 10 presented an automated model for detecting plant diseases in corn and potato leaves.The model utilized local ternary patterns (LTP), segmented fractal texture analysis (SFTA), and histogram-oriented gradient (HOG) as key features.To address the issue of high dimensionality, principal component analysis (PCA) and entropy skewness-based score values were used.While the system's performance relies on the selected features, it may experience reduced accuracy in cases where an insufficient number of features are available.Durairaj et al. 11 proposed a plant disease detection model that incorporates segmentation and an autoencoder technique to improve accuracy.The model began with noise removal through pre-processing, followed by segmentation using the Fuzzy C-means (FCM) algorithm.Features within the segmented area were then extracted using a discrete wavelet transform based on GLCM.However, the model's drawback lies in its lower accuracy.Hossain et al. 12 introduced a method based on color and texture, employing a KNN classifier for plant leaf disease detection and classification.Texture features were extracted from images of diseased leaves for classification purposes.The KNN Classifier was used to classify diseases such as canker, leaf spot, alternate, and bacterial blight, resulting in improved accuracy.However, the dataset used was relatively small.Mahmoud et al. 13 proposed a novel approach for classifying plant diseases using the PILAE algorithm and DCGAN.The PILAE algorithm trains a MLP neural network, while DCGAN performs feature extraction and generates synthetic samples for the minor classes.The classification is then performed using PILAE.However, this model has the drawback of requiring additional time for processing.Pardede et al. 14 introduced an alternative unsupervised learning algorithm based on a convolutional autoencoder for plant disease recognition.The network first learns and identifies discriminative features without the need for data labelling.An SVM-based classifier is then used to classify the encoded features.This approach achieved better accuracy but with reduced robustness.Ramesh et al. 15 proposed a machine learning approach for plant disease detection.They utilized a Random Forest classifier to identify infected and healthy leaves, and extracted features from images using the Histogram of Oriented Gradient (HOG) technique.
Shrivatsava et al. 16 devised a rapid and efficient system to automatically identify and categorize diseases in rice plants.In this study, color played a crucial role, and a polynomial order-2 kernel function was employed in an SVM classifier for classification purposes.However, this system only considers a limited number of disease classes.In addition to an electron nose, a hybrid intelligent system incorporating SVM, probabilistic neural network (PNN), naïve Bayes, and fuzzy interference system was utilized for detection 17 .Furthermore, this system has been found to be time-consuming.Trang et al. 18 introduced the use of an autoencoder as a feature extraction method for plant leaf disease detection, employing a dataset of leaf images.Initially, the original input leaf image was reconstructed using the encoder, and the features were extracted through the encoder.These extracted features were then fed into the SVM classifier for classification.Consequently, improved accuracy was achieved, albeit with increased computational processes.Table 1 lists out the ML based approaches for plant diseases classification with its limitation.

Deep learning (DL) based techniques for plants disease identification
Chohan et al. 27 presented a highly effective neural network model to identify plant diseases.To increase the sample size, they initially performed data augmentation.Then, they applied a CNN with pooling and multiple convolution layers.As a result, the DL model achieved superior performance in detecting plant diseases.However, this model has two main drawbacks: overfitting issues and improved accuracy.Huang 28 proposed a modified DL model for detecting and classifying grapevine diseases.In this DL model, they also utilized transfer learning with pre-trained machine learning approaches.The target diseases for classification and detection were phylloxera, measles, leaf blight, and black rot.Despite achieving maximum classification accuracy, the computation time was longer.Liu et al. 29 introduced an enhanced deep convolutional neural network (DCNN) approach for efficient grape disease detection.They first analyzed the features of grape disease to improve the CNN.Then, they employed deep separable convolution to reduce the number of parameters and mitigate overfitting.The inception structure was utilized to enhance the capability of multiscale feature extraction.However, a limitation of this method is its lack of diversity.
Jun et al. 30 proposed an enhanced v3 YOLO Convolutional neural network for the identification of tomato diseases.The dataset utilized in this study consists of tomato diseases and pests captured in a natural environment.Marino et al. 31 introduced a novel DL model designed for the detection and localization of potato blemishes.Initially, the CNN was trained to categorize potato images, serving as a filter for selecting faces.Subsequently, an integrated SVM and autoencoder were applied to the chosen image to identify damage and greening disease in a patch-wise manner.However, this model is not suitable for real-time applications and is limited in its applicability to other plant diseases.Khamparia et al. 32 developed a hybrid deep convolutional autoencoder network for the prediction and classification of seasonal crop diseases by combining a CNN and an autoencoder.The convolutional autoencoder network plays a crucial role in identifying crop diseases from the input crop image.
Ferentinos et al. 33 introduced a CNN model to diagnose and detect plant diseases by utilizing images of both diseased plants and healthy leaves.Singth et al. 34 developed a hybrid feature-based method for disease detection in plant leaves.This method combines color, texture, and deep features to form hybrid features, which are then classified using a random forest algorithm after data augmentation and Bayesian optimized support vector classifier.Lu et al. 35 presented a deep CNN model specifically designed for automatically detecting and classifying rice diseases.The dataset used in their study consisted of 25  www.nature.com/scientificreports/layers.Additionally, a tenfold cross-validation scheme was employed to enhance accuracy.To further improve the recognition rate, a Boltzmann machine and deep learning techniques were applied.However, it is important to note that a substantial amount of data is necessary to achieve better outcomes in this context.Dhaka et al. 36 conducted an extensive review of the current literature on the use of deep CNNs in predicting plant diseases from leaf images.The study provides valuable insights into pre-processing methods, CNN models, frameworks, optimization techniques, datasets, and performance measures, serving as a valuable reference for researchers navigating the complexities of selecting appropriate models in the agricultural sector.Wang et al. 37 introduced the (Mobile Ghost Attention) MGA-YOLO algorithm for detecting apple diseases, which is a lightweight one-stage network.In this work, the authors replaced standard convolution with the ghost module to reduce the number of parameters and floating-point operations.They combined Mobile Inverted Residual bottleneck convolution with the YOLO network to enhance performance.Morbekar et al. 38 evaluated YOLObased algorithms for crop disease detection, achieving higher accuracy compared to other conventional models.This model can identify single or multiple infection regions on leaves.Among various deep learning algorithms, CNNs are the most widely used.Advanced methods like VGG 16, ResNet, and DenseNet have shown superior results.Additionally, Ferentinos 33 achieved a remarkable accuracy of 99.53% using DL techniques.Table 2 lists out the DL based approaches for plant diseases classification with its limitation.Consequently, DL approaches continue to offer more effective solutions for detecting plant diseases compared to ML methods.
This section extensively explores deep learning and machine learning models for diagnosing plant diseases.The deep learning model exhibits superior accuracy when compared to the machine learning model.Existing literature indicates that the current deep learning models for plant disease detection are based on pre-trained deep convolutional neural networks, which have been trained using benchmark color images.However, finetuning or applying transfer learning to these pre-trained neural networks can result in accuracy issues for certain plant classes.Consequently, there is a growing demand for novel deep convolutional neural networks specifically designed for different plant datasets.The need of the hour is a unique model that can effectively detect various types of plant diseases.This paper proposes a deep convolutional neural architecture that caters to the detection of all kinds of plant diseases.

Proposed HerbNet framework
The proposed deep learning framework comprises of two main phases: the model development phase and the meta-visualization phase.The model development phase involves a three-step process which includes feature extraction, training, and validation.In order to carry out the training and validation, a dataset containing plant leaves is utilized.Figure 1 illustrates the proposed framework for identifying plant diseases.
The images provided are in jpeg format and possess a resolution of 1600*1200.Subsequently, these images undergo resizing to 224×224 utilizing the red, green, and blue channels.The dataset is divided into 70% for training purposes and 30% for validation.

KNN for classification
K-nearest Neighbor (KNN) is a supervised classification algorithm that utilizes the concept of finding similarities between data points to make predictions.It is commonly employed for classification tasks, although it can also be applied to regression problems.The fundamental assumption of KNN is that the data points either form clusters or are located in close proximity to each other.Notably, KNN is a non-parametric algorithm that refrains from making any assumptions about the data.Multiclass classification is considered for solving the proposed problem.
Consider N , the total number of leaf images and N i the number of images in each class i where i = 1,2, ..38.
where, V (x) is the multidimensional feature space with radius being the distance to the k-nearest samples.Then compute, Compute the posterior probability as,

Explainable AI for meta visualizations
The use of an explainable AI not only provides high accuracy, but also provides physiological insight into model predictions, thus generating confidence in model predictions.These explained predictions lend themselves for eventual use in precision agriculture and research application using automated plant diseases classification.In this work, the gradient based and occlusion based explainable AI techniques are developed for meta visualization of plant diseases classification.

Gradient based visualization
The Grad-CAM approach uses gradient information from the Convolutional Neural Network's (CNN) final convolutional layer to assign meaningful values to each neuron.We compute the gradient score for the class y c based on feature map activations A k of a convolutional layer to compute the class-discriminative localization map Grad-CAM of width u and height v for a class c .The neuron significance weight is calculated based on Eq. 1.
This weight a c k is a partial linearization of the deep network downstream from A that captures the significance of feature map k for a target class c.As a result, we execute a weighted combination of forward activation maps to get the Grad-CAM of class c , as shown in Eq. 2.
Our exclusive attention to the qualities that favorably influence the class of interest motivates the use of a Rectified Linear Unit (ReLU) to the linear combination of maps.Specifically, we aim to enhance the intensity of pixels that contribute to the increase of y c .Conversely, pixels with negative values are more likely to pertain to other categories within the image.

Occlusion sensitivity based network interpretation
We have utilized the occlusion sensitivity analysis (OSA), an efficient perturbation-based technique.This approach first quantifies the little variations in the class score by excluding various areas of the input image and making modest adjustments.The next step is to combine the differences in score for each region to create a saliency map for the input image, also known as a sensitivity map.The local image areas in this sensitivity map that show much variance are emphasized as the factors that positively affect the class score.Consequently, the occlusion sensitivity map offers insightful information about the picture characteristics that influence the final judgment and highlights the causes of the network's classification failure.Meaningful Perturbation and Extremal Perturbation produce an opposite-natured saliency map from the OSA.These techniques preserve the components or areas that contribute significantly while hiding the components or regions that contribute less.
(1) www.nature.com/scientificreports/Let I t be the test image with size H × W × 3 where H is the height, and W is the width of red, blue, and green color channels.The first step generates the occlusion masks Ω based on the trained image set.An occlusion mask represents the movement of an anchor point or an object.Applying an occlusion mask i causes a considerable change in the output score, and the relevant occluded regions are shown as output.Measurements of the cooccurrence between occlusion masks may be made using various methods.We gauge co-occurrence based on the displacement vectors' fluctuation pattern as determined by optical flow.We define the co-occurrence between the occlusion masks i, j as represented in Eq. 3. where, for each trained image set anchor point.Mask integration: We combine occlusion masks based on co-occurrence.We combine the K highly cooccurring masks with the i th mask Ω i .In order to construct the integration mask i and ensure that the masks obscure all target regions, we apply the element-wise product.The output score of the target class is then calculated after feeding the occluded test picture into a classification algorithm.If the output score drops, we assume that the occluded regions are crucial for the categorization.The weighted total of the mask for the visualization map S is as shown in Eq. 4.
where f is a model for deep classification.

Results and discussion
The model was implemented using the MATLAB software 48 with version 2020b on a workstation that had an NVIDIA GPU and 16GB RAM.For this study, the researchers selected the Plant village dataset as the benchmark.The same dataset was used to both train and evaluate the proposed framework.This dataset consists of 1,63,000 images that are divided into 38 classes, making it an unbalanced dataset.

Performance analysis of feature extraction phase
The deep neural network has been optimized to efficiently extract features from the pooling layer.The primary goal of the pooling layers is to reduce the dimensions of the hidden layer by combining the outputs of neuron clusters from the previous layer into a single neuron.This reduction in size effectively decreases the number of parameters that need to be learned and reduces the computational workload within the network.Furthermore, the pooling layer effectively summarizes the characteristics produced by a convolution layer within a specific region of the feature map.
Figure 3 presents the t-SNE plot, which showcases the extracted features (25 features alone for improved visualization) for all 30 classes.One significant advantage of t-SNE is its ability to preserve the local structure.
(3) In other words, data points that are close to each other in the high-dimensional dataset will appear close to each other in the chart.Additionally, t-SNE generates visually appealing visualizations.

Performance analysis of classification phase
Customized KNN classification attains the utmost level of precision.A summary in matrix form is presented in Fig. 4, which exhibits a confusion chart.This chart visually represents the count of accurate and inaccurate predictions for each label.Remarkably, it demonstrates a 100% accuracy rate across all labels.The overall performance of the method is evaluated using the ROC curve.This curve aids in determining the optimal cut-off value for assessing the presence of each label.The ROC plot of the proposed model is showcased in Fig. 5.The ROC curve is a probability curve, and the AUC (Area Under the Curve) signifies the model's capability to differentiate between classes.Figure 5 reveals that the AUC is optimal for each label.
In order to create the curve, it is necessary to plot the False Positive Rate (FPR) against the True Positive Rate (TRP).The model's effectiveness can be assessed by calculating the Area Under Cover, which is obtained from the ROC.The parallel plot, also known as the parallel coordinates plot, allows for the comparison of characteristics across multiple individual observations using numerical variables.Each vertical barrepresents a variable and typically has its own scale.This concept is illustrated in Fig. 6.

Performance analysis of the visualization phase
The occlusion sensitivity technique generates a visual representation that shows how the classification score for a specific target class changes when certain parts of the input image are concealed using a mask.This is shown in Fig. 7. On the other hand, Grad-CAM uses the gradient of the classification score for the convolutional features identified by the network to identify the essential areas of the image for classification.This is depicted in Fig. 7.This technique of gradient attribution produces maps that highlight the pixels that are most important for the network's classification.

Comparative analysis with other plant diseases classification models
In this section, the performance of HerbNet is assessed by comparing it with other existing methods for categorizing plant diseases.The Mendeley dataset is utilized to train and validate HerbNet, and the deep learning model constructed on the same dataset is contrasted with the suggested model in terms of training and validation performance.Recently, researchers have devised various alternative approaches to identify plant diseases using leaf photographs.The comparison results of the suggested model, including accuracy and other performance parameters, are presented in Table 3. Table 3 demonstrates that, in comparison to all other SOTA models, the

Conclusion
In this research, we present a novel neural architecture that is specifically designed to identify plant diseases in a deep and explainable manner.Our approach involves extracting deep features from a down sampled feature map of a fine-tuned neural network.These features are then classified using a customized K-Nearest Neighbors Algorithm.To ensure the effectiveness of our model, we train and validate it using the largest standard plant village dataset, which comprises 38 classes.In order to assess the performance of our proposed system, we measure specificity, sensitivity, accuracy, and AUC.The findings reveal that our system achieves an outstanding maximum validation accuracy of 99.95% and an AUC of 1.This establishes our approach as the most optimal and highest-performing method when compared to current state-of-the-art deep learning techniques for automatically identifying plant diseases.In future, the proposed model will be integrated as mobile app with real time images to assist the farmers to identify the plant diseases in the affordable and efficient manner.

Ethical approval
The above work is not based on animal or real-time human data.It is based on the data from the public repository.
www.nature.com/scientificreports/Deep feature extraction Deep Convolutional Neural Networks (DCNN) have made remarkable advancements in image analysis, surpassing conventional machine learning models in feature extraction, classification, and segmentation.DCNNs excel at extracting both low-level and high-level features, where the initial layers focus on low-level features and the upper layers' capture complex high-level features.These extracted features can be utilized for classification using either deep classifiers or traditional classifiers.To extract intricate high-level features from images, the Efficient-NetB0 architecture is employed.Unlike densely packed neural network architectures, this architecture implements consistent compound scaling across all image dimensions.The pooling layer further extracts deep and condensed features.With a mere 5.3 million trainable parameters, this architecture significantly reduces training time compared to other densely packed architectures.The input layers accept RGB images of size 224 × 224.By leveraging this network, the proposed architecture effectively extracts features from images, resulting in an output of a feature vector with a size of 1280 from the pooling layer.The feature extraction phase comprises of 16 Mobile Inverted Bottleneck Convolutional Layers (MBConv) with kernel sizes of 3 × 3 or 5 × 5, as depicted in Fig. 2.

Figure 3 .
Figure 3. t-SNE plot of the features extracted from each class of plant disease images.

Figure 4 .
Figure 4. HerbNet-Confusion Matrix for all 38 classes of plant disease images.

Figure 5 .
Figure 5. HerbNet-RoC plot for each type of plants.

Figure 6 .
Figure 6.Parallel coordinate plot for the first 10 features of all 38 classes of images.

Figure 7 .
Figure 7. HerbNet Meta Visualizations of Pooling features of Apple, corn and cherry sub classes.

Table 1 .
plant species with 58 distinct classes.However, this CNN model faces challenges such as class imbalance, overfitting, and exploding gradient.Despite these challenges, the deep CNN model proposed by Lu et al. effectively diagnoses ten types of rice diseases and includes multiple State of the art machine learning approaches for plant disease classification and its performance analysis.

Table 2 .
State of the art deep learning approaches for plant disease classification and its performance analysis.

Table 3 .
Comparative analysis of the proposed model with other State of the art models for plant disease classsifications.